Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group



DelPhi Force Electrostatic force calculation web server


Delphi Force is a DelPhi-based script, allowing to calculate the electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.

The calculation only requires two PQR files of the two objects. These file can be generated by our DelPhipKa webserver.

This server outputs the forces on each individual residue, and generates pictures to visualize the forces using arrows. In the pictures, the blue arrow shows the total force, the red arrows show the forces on individual residues. The server also provides VMD TCL scripts for the users to make their own pictures.

For questions and help, visit http://compbio.clemson.edu/forum/ or email to delphi@g.clemson.edu

If the use of DelPhi Force results to a publication, please cite:
Li, Lin; Chakravorty, Arghya; Alexov, Emil; Journal of Computational Chemistry, 2017, 38, 584–593. DOI: 10.1002/jcc.24715
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.


Back View
Structure of Calmodulin in calcium loaded and peptide free state (PDB: 5E1K). N-terminal lobe, C-terminal lobe and calcium ions are colored as grey, cyan and orange. The total electrostatic force is shown as blue arrow and the forces applied on each residue are represented as red arrow (The size of the arrows are adjusted for the best visualization).
Right View
Structure of p53 core domain in complex with DNA (PDB: 4HJIE). The p53 core domain binds to DNA as a cooperative tetramer and each monomer is shown as different color. The p53 core domains were moved 20 Å away from DNA along the mass center. The total electrostatic force is shown as blue arrow and the forces applied on each residue are represented as red arrow (The size of the arrows are adjusted for the best visualization).

DelPhi Force calculates the forces of atoms/residues on the "target" molecule under the electrostatic field generated by the "reference" molecule. For more detailed instructions, please check our paper and tutorial.

To calculate forces between two residues or a group of residues in a "reference" structure, use the Residues(s) Pairwise Interaction mode.

Standard PQR format contains the following information for each atom: index, name, residue name, 3D coordinates, charge, radius. You can generate a PQR file using a PDB file and our DelPhipKawebserver. This will allow you to create a PQR at desired pH.

Here we provide a sample PQR file: link





DelPhi Force calculates the forces of atoms/residues on the "target" molecule under the electrostatic field generated by the "reference" molecule. For more detailed instructions, please check our paper and tutorial.

To calculate forces between two residues or a group of residues in a "reference" structure, use the Residues(s) Pairwise Interaction mode.

Standard PQR format contains the following information for each atom: index, name, residue name, 3D coordinates, charge, radius. You can generate a PQR file using a PDB file and our DelPhipKawebserver. This will allow you to create a PQR at desired pH.

Here we provide a sample PQR file: link






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